Contacts of the helix formed by residues 49 - 68 (chain 1) in PDB entry 3TDD
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 49 (chain 1).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-31 VAL* 2.6 44.4 + - + +
-21 THR* 3.9 4.3 - - - +
-11 GLY* 3.8 22.9 - - - +
201 GLY* 4.6 4.7 - - - -
311 VAL* 4.3 17.7 - - + -
331 ARG* 4.3 2.7 - - - -
451 ILE 5.9 0.2 - - - +
461 SER 6.1 0.4 - - - -
471 GLY 3.8 2.7 - - - +
481 ASP* 1.3 69.4 - - - +
501 SER* 1.3 66.5 + - - +
521 MET* 3.1 30.7 + - + +
531 GLN* 3.0 39.7 + - - +
1182 SER* 4.3 2.0 - - - -
1202 HIS* 4.1 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 50 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-31 VAL* 4.6 1.4 + - - +
481 ASP* 2.5 21.5 + - - -
491 ILE* 1.3 77.8 - - - +
511 ASP* 1.3 60.5 + - - +
531 GLN* 3.3 6.0 + - - +
541 HIS* 3.1 16.5 + - - +
842 LYS* 4.7 2.3 + - - -
882 TYR* 3.3 21.4 - - - -
912 LYS* 3.0 20.8 + - - -
1162 GLY* 3.5 10.2 + - - -
1182 SER* 3.6 37.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 51 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-71 GLN* 3.1 19.1 + - - +
481 ASP* 2.9 14.4 + - + +
501 SER* 1.3 80.1 + - - +
521 MET* 1.3 65.3 + - - +
541 HIS* 3.0 4.4 + - - +
551 ILE* 2.9 25.3 + - - +
901 ARG* 5.3 0.5 + - - -
941 PRO 4.8 0.4 - - - -
951 LEU* 3.5 16.5 - - + +
961 TRP* 2.9 26.2 + - - +
971 ASN* 3.3 19.1 - - - +
882 TYR* 2.8 29.4 + - - -
912 LYS* 3.4 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 52 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311 VAL* 4.1 16.4 - - + -
321 GLU 3.7 17.3 - - - +
331 ARG* 4.0 31.2 - - - -
351 ILE* 4.6 5.4 - - + -
451 ILE* 3.6 42.9 - - + +
461 SER 6.2 0.2 - - - -
481 ASP 3.0 14.2 + - - +
491 ILE* 3.1 31.4 + - + +
511 ASP* 1.3 76.5 - - - +
531 GLN* 1.3 56.1 - - + +
551 ILE* 3.0 8.9 + - - +
561 GLU* 2.8 47.7 + - - +
971 ASN* 4.0 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 53 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491 ILE* 3.0 26.4 + - + +
501 SER* 3.5 6.0 - - - +
511 ASP 3.3 0.2 - - - -
521 MET* 1.3 83.6 - - + +
541 HIS* 1.3 61.3 + - - +
561 GLU* 3.2 16.9 - - - +
571 ARG* 3.1 21.7 + - - +
842 LYS* 3.4 20.0 + - - +
1182 SER* 3.4 13.8 - - - -
1192 VAL* 2.9 47.7 + - - +
1202 HIS* 4.3 3.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 54 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501 SER 3.1 8.4 + - - +
511 ASP 3.0 8.0 + - - +
531 GLN* 1.3 74.7 - - - +
551 ILE* 1.3 68.3 + - - +
571 ARG* 3.1 36.1 + - - +
581 LEU* 3.0 50.8 + - + +
861 VAL* 5.9 0.4 - - - +
901 ARG* 4.2 13.2 + - - -
951 LEU* 3.8 26.6 - - + +
842 LYS* 5.6 4.9 - - - +
882 TYR* 3.3 32.4 - + + +
892 GLU* 5.7 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 55 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451 ILE* 3.9 18.2 - - + -
511 ASP 2.9 14.6 + - - +
521 MET* 3.0 8.9 + - - +
541 HIS* 1.3 74.3 - - + +
561 GLU* 1.3 65.2 + - - +
581 LEU* 3.1 12.3 + - + +
591 LEU* 3.0 29.2 + - + +
831 LEU* 3.7 30.1 - - + -
871 MET* 4.7 0.9 - - - -
951 LEU* 4.1 26.7 - - + -
971 ASN* 3.5 28.0 - - - +
991 ILE* 3.8 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 56 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321 GLU 4.9 2.6 - - - +
351 ILE* 3.5 34.6 - - + +
451 ILE* 5.2 0.8 - - - +
521 MET* 2.8 27.5 + - - +
531 GLN* 3.2 24.0 - - - +
551 ILE* 1.3 78.6 - - - +
571 ARG* 1.3 60.2 + - - +
591 LEU* 3.3 12.0 + - - +
601 LYS* 3.2 46.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531 GLN 3.1 12.4 + - - +
541 HIS* 3.1 36.3 + - - +
561 GLU* 1.3 74.1 - - - +
581 LEU* 1.3 72.6 + - - +
601 LYS* 3.4 11.0 + - + +
611 ASP* 2.8 54.6 + - - +
842 LYS* 6.3 2.5 - - - +
852 GLU* 5.6 2.4 + - - -
101T LYS* 3.4 56.2 - - - +
104T LYS* 6.5 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541 HIS* 3.0 50.7 + - + +
551 ILE* 3.1 17.7 + - + +
571 ARG* 1.3 89.5 - - - +
591 LEU* 1.3 58.4 + - + +
611 ASP* 3.4 9.1 + - + +
621 LEU* 3.0 27.0 + - - +
821 TYR* 4.1 33.2 + - + +
831 LEU* 5.3 3.6 - - + -
861 VAL* 4.6 20.2 - - + -
951 LEU* 5.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 59 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351 ILE* 3.8 28.0 - - + -
371 VAL* 4.0 19.4 - - + +
431 VAL* 4.3 14.6 - - + -
451 ILE* 5.3 0.4 - - + -
551 ILE* 3.0 33.5 + - + +
561 GLU* 3.5 7.2 - - - +
571 ARG 3.2 0.2 - - - -
581 LEU* 1.3 75.3 - - - +
601 LYS* 1.3 66.4 + - + +
611 ASP 3.1 1.6 - - - -
621 LEU* 3.1 27.3 + - + +
631 VAL* 3.1 17.3 + - - +
791 ILE* 3.8 27.4 - - + -
821 TYR* 5.1 0.4 - - + -
831 LEU* 4.3 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 60 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561 GLU* 3.2 33.3 + - - +
571 ARG* 3.4 14.1 + - + +
591 LEU* 1.3 77.5 - - + +
611 ASP* 1.3 64.7 + - - +
631 VAL* 3.3 4.4 + - - +
641 THR* 3.0 19.9 + - - +
72T ARG* 3.0 21.6 + - - +
104T LYS* 5.1 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 61 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571 ARG* 2.8 37.4 + - - +
581 LEU* 3.5 12.7 - - + +
591 LEU 3.1 0.2 - - - -
601 LYS* 1.3 77.3 - - - +
621 LEU* 1.3 68.5 + - - +
641 THR* 3.1 8.0 + - - -
651 GLU* 2.7 38.9 + - - +
97T ALA* 5.3 8.5 - - - +
100T LYS* 5.5 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371 VAL* 5.8 0.7 - - + -
581 LEU 3.0 9.6 + - - +
591 LEU* 3.1 23.8 + - + +
611 ASP* 1.3 74.4 - - - +
631 VAL* 1.3 58.7 + - - +
651 GLU* 3.3 6.8 + - + +
661 ASN* 2.8 32.4 + - + +
741 LEU* 4.0 22.7 - - + -
791 ILE* 4.4 24.2 - - + -
821 TYR* 3.6 39.3 - - + -
103S PHE* 3.6 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 63 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371 VAL* 4.0 14.8 - - + -
381 GLY* 5.0 8.7 - - - +
591 LEU 3.1 12.5 + - - +
601 LYS* 3.4 9.6 - - - +
621 LEU* 1.3 75.5 - - - +
641 THR* 1.3 65.8 + - - +
661 ASN* 3.0 14.0 + - - +
671 ALA* 3.1 14.0 + - + +
741 LEU* 3.9 22.0 - - + -
72T ARG* 3.3 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 64 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601 LYS 3.0 7.2 + - - -
611 ASP* 3.5 10.8 + - - -
631 VAL* 1.3 77.8 - - - +
651 GLU* 1.3 66.6 + - - +
671 ALA* 3.2 19.9 + - - +
681 TYR* 3.4 35.5 + - + +
71T ASP* 3.7 24.5 - - - +
72T ARG* 2.7 35.8 + - - +
100T LYS* 4.7 7.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 65 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611 ASP* 2.7 32.8 + - - +
621 LEU* 3.7 7.6 - - + +
641 THR* 1.3 72.0 - - - +
661 ASN* 1.3 62.6 + - - +
671 ALA 3.0 4.9 - - - -
681 TYR* 3.0 46.7 + - + +
111S ARG* 6.3 0.4 - - - +
93T ARG* 5.6 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 66 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621 LEU* 2.8 22.3 + - + +
631 VAL* 3.6 4.3 - - - +
651 GLU* 1.3 72.0 - - - +
671 ALA* 1.3 57.5 + - - +
681 TYR 3.4 0.4 - - - +
701 ASN* 3.0 44.0 + - - +
711 GLU* 3.0 32.9 + - - +
741 LEU* 3.8 26.1 - - + +
105S ARG* 2.8 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 67 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631 VAL* 3.1 10.8 + - + +
641 THR* 3.3 14.6 - - - +
651 GLU 3.0 0.6 - - - -
661 ASN* 1.3 78.3 - - - +
681 TYR* 1.3 66.7 + - + +
691 ASP 3.2 1.4 + - - -
701 ALA* 3.1 34.4 + - + +
69T VAL* 4.5 10.2 - - + +
71T ASP 5.7 2.0 - - - +
72T ARG* 5.8 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 68 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641 THR* 3.6 20.8 - - + +
651 GLU* 3.0 43.8 + - + +
661 ASN 4.2 0.3 - - - +
671 ALA* 1.3 76.6 - - + +
691 ASP* 1.3 69.0 + - - +
701 ASN* 3.0 5.7 + - - +
111S ARG* 5.7 5.0 + - - -
69T VAL* 3.4 25.1 - - + -
71T ASP* 2.6 51.4 + - - -
93T ARG* 3.5 54.7 + - + +
96T ALA* 5.5 0.7 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il